LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task clear OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task # The units we assume we'll use. The kim-lammps-preprocessor # may swap this line out if running against a Simulator Model # whose units are not 'metal' units metal # Variables that can be adjusted by kim-lammps-preprocessor# to switch unit sets for Simulator Models variable _u_distance equal 1.0 variable _u_energy equal 1.0 variable _u_mass equal 1.0 variable _u_pressure equal 1.0 dimension 3 boundary p p p # This line may be swapped out by kim-lammps-preprocessor if # running against a Simulator Model whose atom_style is not # 'atomic' atom_style atomic # Adjust input variables for possible units changes with Simulator Models variable lattice_constant_converted equal 3.987558534741402*${_u_distance} variable lattice_constant_converted equal 3.987558534741402*1 variable xmin_converted equal 0.0*${_u_distance} variable xmin_converted equal 0.0*1 variable xmax_converted equal 40.07446730609016*${_u_distance} variable xmax_converted equal 40.07446730609016*1 variable ymin_converted equal -40.0784548646249*${_u_distance} variable ymin_converted equal -40.0784548646249*1 variable ymax_converted equal 40.0784548646249*${_u_distance} variable ymax_converted equal 40.0784548646249*1 variable zmin_converted equal 0.0*${_u_distance} variable zmin_converted equal 0.0*1 variable zmax_converted equal 3.987558534741402*${_u_distance} variable zmax_converted equal 3.987558534741402*1 lattice fcc ${lattice_constant_converted} lattice fcc 3.9875585347414 Lattice spacing in x,y,z = 3.98756 3.98756 3.98756 region whole block ${xmin_converted} ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 ${xmax_converted} ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 40.0744673060902 ${ymin_converted} ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 40.0744673060902 -40.0784548646249 ${ymax_converted} ${zmin_converted} ${zmax_converted} units box region whole block 0 40.0744673060902 -40.0784548646249 40.0784548646249 ${zmin_converted} ${zmax_converted} units box region whole block 0 40.0744673060902 -40.0784548646249 40.0784548646249 0 ${zmax_converted} units box region whole block 0 40.0744673060902 -40.0784548646249 40.0784548646249 0 3.9875585347414 units box create_box 2 whole Created orthogonal box = (0 -40.0785 0) to (40.0745 40.0785 3.98756) 1 by 1 by 1 MPI processor grid region upper block INF INF 0.0 ${ymax_converted} INF INF units box region upper block INF INF 0.0 40.0784548646249 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 -1 0 orient y 1 10 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 10 -1 0 orient y 1 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.36455 4.36455 3.98756 create_atoms 1 region upper Created 406 atoms create_atoms CPU = 0.000227928 secs group upper type 1 406 atoms in group upper mass 1 26.981538*${_u_mass} mass 1 26.981538*1 displace_atoms upper move 4.522444029504401 0 0.3333333333333333 units lattice region lower block INF INF ${ymin_converted} 0.0 INF INF units box region lower block INF INF -40.0784548646249 0.0 INF INF units box lattice fcc ${lattice_constant_converted} orient x 10 1 0 orient y -1 10 0 orient z 0 0 1 lattice fcc 3.9875585347414 orient x 10 1 0 orient y -1 10 0 orient z 0 0 1 Lattice spacing in x,y,z = 4.36455 4.36455 3.98756 create_atoms 2 region lower Created 406 atoms create_atoms CPU = 9.20296e-05 secs group lower type 2 406 atoms in group lower displace_atoms lower move -4.522444029504401 0 -0.3333333333333333 units lattice mass 2 26.981538*${_u_mass} mass 2 26.981538*1 pair_style kim EAM_Dynamo_JacobsenNorskovPuska_1987_Al__MO_411692133366_000 pair_coeff * * Al Al variable neigh_skin_converted equal 2.0*${_u_distance} variable neigh_skin_converted equal 2.0*1 neighbor ${neigh_skin_converted} bin neighbor 2 bin neigh_modify delay 10 check yes variable delete_distance equal 0.5*${lattice_constant_converted} variable delete_distance equal 0.5*3.9875585347414 delete_atoms overlap ${delete_distance} all all delete_atoms overlap 1.9937792673707 all all Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 21 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 796 min_style cg minimize 1e-15 1e-15 5000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.947 | 4.947 | 4.947 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2670.8006 0 -2670.8006 484.44589 251 0 -2685.6824 0 -2685.6824 -9077.8245 Loop time of 1.2206 on 1 procs for 251 steps with 796 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2670.80055542 -2685.68241507 -2685.68241507 Force two-norm initial, final = 18.2065 1.2793e-06 Force max component initial, final = 5.89001 1.77403e-07 Final line search alpha, max atom move = 1 1.77403e-07 Iterations, force evaluations = 251 490 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1924 | 1.1924 | 1.1924 | 0.0 | 97.69 Neigh | 0.0026071 | 0.0026071 | 0.0026071 | 0.0 | 0.21 Comm | 0.016304 | 0.016304 | 0.016304 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009336 | | | 0.76 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5844 ave 5844 max 5844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108820 ave 108820 max 108820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108820 Ave neighs/atom = 136.709 Neighbor list builds = 1 Dangerous builds = 0 fix 1 all box/relax x 0.0 z 0.0 couple none vmax 0.001 minimize 1.0e-25 1.0e-25 1000 10000 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Per MPI rank memory allocation (min/avg/max) = 4.948 | 4.948 | 4.948 Mbytes Step Temp E_pair E_mol TotEng Press Volume 251 0 -2685.6824 0 -2685.6824 -9077.8245 12809.017 1251 0 -2685.9776 0 -2685.9776 -1462.8367 12700.948 Loop time of 4.57481 on 1 procs for 1000 steps with 796 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -2685.68241507 -2685.97760573 -2685.97760578 Force two-norm initial, final = 91.6432 0.0179158 Force max component initial, final = 70.2301 0.0117388 Final line search alpha, max atom move = 0.0682238 0.000800863 Iterations, force evaluations = 1000 1993 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3164 | 4.3164 | 4.3164 | 0.0 | 94.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.058879 | 0.058879 | 0.058879 | 0.0 | 1.29 Output | 5.6982e-05 | 5.6982e-05 | 5.6982e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1994 | | | 4.36 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5854 ave 5854 max 5854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109112 ave 109112 max 109112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109112 Ave neighs/atom = 137.075 Neighbor list builds = 0 Dangerous builds = 0 unfix 1 # Variables used to rescale the positions and energies so that the quantities # in the dumpfile are in the original metal units (angstrom and eV) # even if we're running with a Simulator Model that uses different units variable pe_metal equal "c_thermo_pe/v__u_energy" variable lx_metal equal lx/${_u_distance} variable lx_metal equal lx/1 variable ly_metal equal ly/${_u_distance} variable ly_metal equal ly/1 variable lz_metal equal lz/${_u_distance} variable lz_metal equal lz/1 variable press_metal equal "c_thermo_press/v__u_pressure" variable pxx_metal equal pxx/${_u_pressure} variable pxx_metal equal pxx/1 variable pyy_metal equal pyy/${_u_pressure} variable pyy_metal equal pyy/1 variable pzz_metal equal pzz/${_u_pressure} variable pzz_metal equal pzz/1 variable mass_metal atom mass/${_u_mass} variable mass_metal atom mass/1 compute csym all centro/atom fcc compute particle_eng all pe/atom compute particle_engsum all reduce sum c_particle_eng compute csymsum all reduce sum c_csym compute distance all pair/local dist compute mindist all reduce min c_distance # Isolated atom energy in eV (no unit conversion necessary) variable isolated_atom_energy equal -1.81000000000002 variable particle_eng_metal atom "c_particle_eng/v__u_energy - v_isolated_atom_energy" variable csym_metal atom c_csym/(${_u_distance}*${_u_distance}) variable csym_metal atom c_csym/(1*${_u_distance}) variable csym_metal atom c_csym/(1*1) variable csymsum_metal equal c_csymsum/(${_u_distance}*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*${_u_distance}) variable csymsum_metal equal c_csymsum/(1*1) variable mindist_metal equal c_mindist/${_u_distance} variable mindist_metal equal c_mindist/1 reset_timestep 0 run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 5.085 | 5.085 | 5.085 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2685.9776 0 -2685.9776 -1462.8367 Loop time of 9.53674e-07 on 1 procs for 0 steps with 796 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5899 ave 5899 max 5899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109472 ave 109472 max 109472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109472 Ave neighs/atom = 137.528 Neighbor list builds = 0 Dangerous builds = 0 thermo 0 thermo_style custom step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal run 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Per MPI rank memory allocation (min/avg/max) = 5.085 | 5.085 | 5.085 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2685.9776 -2685.9776 39.759793 80.15691 3.9852085 -1462.8367 -1462.8367 -0.7333189 -4386.2968 -1.4799291 2.5130014 290.68266 Loop time of 9.53674e-07 on 1 procs for 0 steps with 796 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5899 ave 5899 max 5899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54736 ave 54736 max 54736 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109472 ave 109472 max 109472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109472 Ave neighs/atom = 137.528 Neighbor list builds = 0 Dangerous builds = 0 variable num_atoms equal "count(all)" print "${num_atoms}" file output/dump_011.4212/numatoms.out 796 variable adjusted_pe_metal equal ${pe_metal}-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2685.97760577591-${num_atoms}*${isolated_atom_energy} variable adjusted_pe_metal equal -2685.97760577591-796*${isolated_atom_energy} variable adjusted_pe_metal equal -2685.97760577591-796*-1.81000000000002 print "${adjusted_pe_metal} eV" file output/dump_011.4212/energy.out -1245.21760577589 eV print "${mindist_metal} Angstroms" file output/dump_011.4212/mindistance.out 2.51300135207652 Angstroms write_dump all cfg output/dump_011.4212/dump_post.cfg mass type xs ys zs id v_mass_metal v_csym_metal v_particle_eng_metal modify element Al Al print "This indicates that LAMMPS ran successfully" file output/dump_011.4212/success.out This indicates that LAMMPS ran successfully Total wall time: 0:00:05